Acetylcholinesterase (AChE) inhibition has been considered a promising temporary treatment for Alzheimer’s disease. The present study was conducted to isolate chemical constituents from the fruit of Citrus unshiu Markovich (Rutaceae) and evaluate their inhibitory effects on AChE. Phytochemical investigation of C. unshiu fruit led to the isolation of methyl nomilinate (1), limocitrunshin (2), nobiletin (3), kaempferol 3-O-rutinoside (4), limocitrin 3-glucoside (5), kaempferol 3-(2G-rhamnosylrutinoside) (6), didymin (7), (2S)-narirutin 4'-O-glucoside (8) and naringenin 7-O-rutinoside (9). The structures were identified with 1H and 13C NMR spectroscopic data and ESI-MS, then comparison of their spectroscopic and physical data with those previously reported, as well as by measurement of their specific rotations. A limonoid, methyl nomilinate (1), inhibited AChE activity by more than 50% at a concentration of 30 μg/ml. The findings in this study provide the first experimental evidence that a limonoid compound 1 from C. unshiu fruit acts as a natural AChE inhibitor.